Gene detail

Detailed information of OS493_000314-T1 in Lophelia pertusa

Genomic Location: scaffold_1:3854933...3857817
NR annotation: KAJ7394500.1, SPRY domain-containing SOCS box protein 4 [Desmophyllum pertusum]
Species Lophelia pertusa · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
A1Z6E0	Protein gustavus OS=Drosophila melanogaster OX=7227 GN=gus PE=1 SV=2
Q9D5L7	SPRY domain-containing SOCS box protein 1 OS=Mus musculus OX=10090 GN=Spsb1 PE=1 SV=1
Q96BD6	SPRY domain-containing SOCS box protein 1 OS=Homo sapiens OX=9606 GN=SPSB1 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0007491 (this species only)
Ubiquitin family	E3\|E3 adaptor Cullin RING\|SOCS · all ubiquitin genes in this species

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF07525 all species →	SOCS_box	SOCS box	Domain	Interproscan
PF00622 all species →	SPRY	SPRY domain	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR001496 all species →	Domain	SOCS box domain	Interproscan
IPR013320 all species →	Homologous_superfamily	Concanavalin A-like lectin/glucanase domain superfamily	Interproscan
IPR043136 all species →	Homologous_superfamily	B30.2/SPRY domain superfamily	Interproscan
IPR001870 all species →	Domain	B30.2/SPRY domain	Interproscan
IPR050672 all species →	Family	F-box/SPRY and SOCS box protein families	Interproscan
IPR003877 all species →	Domain	SPRY domain	Interproscan
IPR036036 all species →	Homologous_superfamily	SOCS box-like domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR12245 all species →	SPRY DOMAIN CONTAINING SOCS BOX PROTEIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0019005 all species →	Cellular Component	SCF ubiquitin ligase complex	Interproscan
GO:0043161 all species →	Biological Process	proteasome-mediated ubiquitin-dependent protein catabolic process	Interproscan
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0035556 all species →	Biological Process	intracellular signal transduction	Interproscan

Search by domain instead of by gene. Any accession above (InterPro, Pfam, PANTHER, GO, KEGG) can be used as a query on the Functional Domain Search page, which searches all 148 annotated genomes at once.

KEGG pathway

KO	Enzyme	Enzyme ID	Pathway	Map ID	Source
K10343	SPSB1_4, SSB1, SSB4; SPRY domain-containing SOCS box protein 1/4	-	Ubiquitin system	ko04121	deepkoala

Searching by KO or pathway ID across all species is available on the KEGG Pathway page.

Expression pattern (RNA-seq)

Transcript abundance of OS493_000314-T1 across 110 RNA-seq samples of Lophelia pertusa. Values are TPM (transcripts per million) from the StringTie quantification; one bar is one sample, grouped and coloured by condition, sorted by expression within each group.

110Samples

110TPM > 0

7Conditions

1,174.1Max TPM

141.6Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	26.43	45.68
polyp at pH7 6	18	18	29.06	53.21
coral polyp · control treatment	16	16	66.71	172.86
coral polyp · oil and dispersant treatment	16	16	125.38	211.58
coral polyp · oil treatment	16	16	61.68	111.40
coral polyp · dispersant treatment	16	16	637.58	1,174.13
Polyp	10	10	31.62	82.62

Per sample · hover a bar for the full sample record · show / hide the sample table

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	45.68
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	42.44
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	38.94
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	36.30
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	34.59
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	32.03
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	26.98
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.94
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.59
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.46
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.36
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.07
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.81
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.49
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.63
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.20
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.18
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.09
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	53.21
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	50.65
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	40.42
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	36.51
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	36.18
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	35.38
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	32.72
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	32.54
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	31.13
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	29.87
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	28.19
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.99
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.37
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.02
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.01
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.75
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.52
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.61
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	172.86
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	99.84
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	97.41
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	91.33
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	74.30
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	72.19
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	65.45
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	64.65
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	57.39
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	54.95
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	54.57
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	43.96
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	34.45
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	31.95
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	28.91
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	23.15
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	211.58
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	201.36
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	165.15
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	160.01
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	156.21
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	153.38
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	131.68
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	119.70
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	119.34
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	101.77
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	101.44
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	95.11
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	85.68
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	84.70
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	59.63
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	59.41
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	111.40
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	97.76
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	92.45
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	89.29
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	79.88
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	77.56
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	59.62
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	59.14
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	55.01
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	53.62
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	51.64
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	47.73
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	45.33
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	38.49
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.55
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.41
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1,174.13
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1,051.36
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	945.40
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	925.13
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	909.59
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	763.31
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	753.66
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	695.37
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	665.12
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	532.98
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	501.93
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	443.67
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	439.59
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	342.85
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	32.33
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	24.88
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	82.62
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	78.22
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	63.74
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	28.87
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	16.01
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	12.00
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	10.93
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	9.88
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	7.93
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	5.96

Source: CnidoSite RNA-seq expression matrices (LPERT_TPM, StringTie quantification over 110 runs), joined to SRA sample metadata. Samples whose tissue/treatment is not recorded in the source metadata are grouped by the descriptor carried in the expression matrix itself.